Pramod Shinde
Associate Research Scientist in PathologyCards
About
Research
Publications
Featured Publications
Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality
Gygi J, Maguire C, Patel R, Shinde P, Konstorum A, Shannon C, Xu L, Hoch A, Jayavelu N, Haddad E, Network I, Reed E, Kraft M, McComsey G, Metcalf J, Ozonoff A, Esserman D, Cairns C, Rouphael N, Bosinger S, Kim-Schulze S, Krammer F, Rosen L, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier C, Steen H, Altman M, Montgomery R, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen K, Fragiadakis G, Becker P, Sekaly R, Ehrlich L, Fourati S, Peters B, Kleinstein S, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. Journal Of Clinical Investigation 2024, 134: e176640. PMID: 38690733, PMCID: PMC11060740, DOI: 10.1172/jci176640.Peer-Reviewed Original ResearchConceptsClinical outcomesImmune cascadeElevated levels of inflammatory cytokinesDisease severityLevels of inflammatory cytokinesFormation of neutrophil extracellular trapsAcute COVID-19 severityCritically ill patientsNeutrophil extracellular trapsDevelopment of therapiesCOVID-19 cohortCOVID-19 severityViral clearanceImmunosuppressive metabolitesDeep immunophenotypingMultiomic modelIFN-stimulated genesImmunophenotypic assessmentB cellsDisease courseEarly upregulationInflammatory cytokinesDisease progressionIFN inhibitorsExtracellular trapsA multi-omics systems vaccinology resource to develop and test computational models of immunity
Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum J, Overton J, Guzman-Orozco H, Nili S, Orfield S, Gygi J, da Silva Antunes R, Sette A, Grant B, Olsen L, Konstorum A, Guan L, Ay F, Kleinstein S, Peters B. A multi-omics systems vaccinology resource to develop and test computational models of immunity. Cell Reports Methods 2024, 4: 100731. PMID: 38490204, PMCID: PMC10985234, DOI: 10.1016/j.crmeth.2024.100731.Peer-Reviewed Original ResearchImpact of modular mitochondrial epistatic interactions on the evolution of human subpopulations
Shinde P, Whitwell H, Verma R, Ivanchenko M, Zaikin A, Jalan S. Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations. Mitochondrion 2021, 58: 111-122. PMID: 33618020, DOI: 10.1016/j.mito.2021.02.004.Peer-Reviewed Original ResearchConceptsCo-mutation networksPresence of epistasisMt genomesAncestral stateGenomic variationMitochondrial haplogroupsCo-mutationsOcean populationsEpistatic interactionsEvolutionary patternsHypervariable regionCOX genesNatural selectionModule analysisHuman subpopulationsEpistasisHierarchical modularityAmerican populationHaplogroupsNucleotideGenesMutationsPopulationHuman history
2025
Brain rewiring during development: A comparative analysis of larval and adult Drosophila melanogaster connectomes
Yadav P, Shinde P, Singh A. Brain rewiring during development: A comparative analysis of larval and adult Drosophila melanogaster connectomes. Network Neuroscience 2025, 9: 1299-1322. PMID: 41280232, PMCID: PMC12635837, DOI: 10.1162/netn.a.26.Peer-Reviewed Original ResearchScale-free regimeBrain networksScale-free patternsRich-clubPower-law distributionDegree distributionStructural coreMushroom body neuronsTopological influenceAdult brain networkAdult fly brainAnalysis of larvalComplex rewiringExponentIn-degreeMushroom bodiesFly brainNeuronal wiringAdult stageBrain rewiringRewiringLarvalAntennal lobeLife stagesNetwork measuresIs the vaccination-induced B cell receptor repertoire predictable?
Richardson E, Willemsen L, Shinde P, Nielsen M, Peters B. Is the vaccination-induced B cell receptor repertoire predictable? ImmunoInformatics 2025, 19: 100057. PMID: 41311460, PMCID: PMC12657037, DOI: 10.1016/j.immuno.2025.100057.Peer-Reviewed Original ResearchB cell receptorB cellsClonal expansionClonal expansion of B cellsPopulation of memory cellsExpansion of B cellsAntigen re-encounterPost-vaccinationB cell receptor repertoiresMemory B cellsHeavy chain repertoireClonotypic expansionVaccine-inducedReceptor repertoireBCR clonotypesClonotypesImmune responseImmune Epitope DatabaseVaccine antigensChain repertoireBooster vaccinationMonoclonal antibodiesVaccineDays postEpitope DatabaseTh1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop
Willemsen L, Lee J, Shinde P, Soldevila F, Aoki M, Orfield S, Kojima M, da Silva Antunes R, Sette A, Peters B. Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop. Nature Communications 2025, 16: 3132. PMID: 40169665, PMCID: PMC11961675, DOI: 10.1038/s41467-025-58460-8.Peer-Reviewed Original ResearchConceptsMemory T cell responsesT cell responsesTh1 polarizationInterferon responseWP primed individualsTdap booster vaccinationCausative agent of whooping coughPredominant Th1 responseAgent of whooping coughT cell polarizationPertussis vaccine responseBordetella pertussisCausative agentMulti-omics approachChemokine levelsWP vaccinesTh1 responseWP primingIFN-gVaccine responseTh1Protective immunityImmune responsePositive feedback loopBooster vaccinationPutting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses
Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel J, Cheng P, Dastidar S, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum J, Guan L, Guan W, Gygi J, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie J, Kojima M, Konstorum A, Lee J, Lewis S, Li A, Lock E, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen L, Orfield S, Overton J, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu C, Ay F, Grant B, Kleinstein S, Peters B. Putting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses. PLOS Computational Biology 2025, 21: e1012927. PMID: 40163550, PMCID: PMC11978014, DOI: 10.1371/journal.pcbi.1012927.Peer-Reviewed Original Research
2023
Higher-order co-mutation interactions in mitochondrial genomes
Verma R, Shinde P, Mishra A, Jalan S. Higher-order co-mutation interactions in mitochondrial genomes. New Journal Of Physics 2023, 25: 093021. DOI: 10.1088/1367-2630/acf51a.Peer-Reviewed Original ResearchMitochondrial genomeND genesCoding genesCo-mutation networksHuman mitochondrial DNAPair-wise interactionsManifestation of phenotypesNuclear genomeGenetic interactionsMitochondrial DNAVariable sitesGenomeAltitude populationsGenesPhenotypic associationsATP6Genetic disordersEnvironmental conditionsCO1Higher-order interactionsCYBDNAPhenotypeInteraction
2022
Nucleotide-based genetic networks: Methods and applications
Verma R, Shinde P, Jalan S. Nucleotide-based genetic networks: Methods and applications. Journal Of Biosciences 2022, 47: 63. PMID: 36226367, PMCID: PMC9554864, DOI: 10.1007/s12038-022-00290-7.Peer-Reviewed Original ResearchConceptsCo-occurrence networkGenetic signaturesHuman mitochondrial genomeStochastic evolutionary forcesMitochondrial genomeFrequency of polymorphismsGenomic variationWhole genomeEvolutionary forcesGenetic networksGenomic networksGenetic variationFundamental processesDNA samplesNucleotideViral evolutionGenomeCo-evolutionHuman migrationPolymorphismBiological mechanismsCo-occurrenceDNAHuman adaptationMigration
2021
Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes
Verma R, Kalyakulina A, Giuliani C, Shinde P, Kachhvah A, Ivanchenko M, Jalan S. Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes. Scientific Reports 2021, 11: 133. PMID: 33420243, PMCID: PMC7794584, DOI: 10.1038/s41598-020-80271-8.Peer-Reviewed Original ResearchConceptsCo-occurring motifsMitochondrial genome levelMt DNA sequencesAltitude adaptationAsian human populationsHigh-altitude adaptationMitochondrial genomeMitochondrial variationHaplogroup analysisCo-occurrence networkGenomic variationMitochondrial DNACo-occurrenceNCBI databaseGenomic levelGene complexNetwork motifsCumulative effect of variationsStructural elementsMotifCo-evolutionHuman populationSimilarity clusteringHigh altitudeHigh-altitude regions